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bioRxiv2017

Modeling The Consequences Of Heterogeneity In Microbial Population Dynamics

Chapter 1The rate at which unicellular micro-organisms progress through the cell cycle is a major component of their evolutionary fitness. Measuring fitness phenotypes in a given environment or genetic background forms the basis of most quantitative assays of drug sensitivity or genetic interaction, including genome-wide assays. Growth rate is typically measured in bulk cell populations, inoculated with anything from hundreds to millions of cells sampled from purified, isogenic colonies. High-throughput microscopy reveals that striking levels of growth rate heterogeneity arise between isogenic cell lineages (Levy et al., 2012). Using published Saccharomyces cerevisiae data, I examine the implications for interpreting bulk, population scale growth rate observations, given observed levels of growth rate heterogeneity at the lineage level. I demonstrate that selection between cell lineages with a range of growth rates can give rise to an apparent lag phase at the population level, even in the absence of evidence for a lag phase at the lineage level. My simulations further predict that, given observed levels of heterogeneity, final populations should be dominated by one or a few lineages.\n\nChapter 2In order to validate and further explore the conclusions from Chapter 1, I re-analyzed high-throughput microscopy experiments carried out on Quantitative Fitness Analysis (QFA) S. cerevisiae cultures (Addinall et al., 2011), an approach referred to as QFA. To allow for precise observation of purely clonal lineages including very fast-growing lineages and non-dividing cells, I re-designed an existing image analysis tool for QFA, now available as an open source Python package. Fast-growing outliers in particular influence the extent of the lag phase apparent at the population level, making the precision of growth rate estimation a key ingredient for successfully simulating population observations. QFA data include population observations which I used to validate the population simulations generated from individual lineage data. I explored various options for modeling lineage growth curves and for carrying out growth rate parameter inference, and included the full workflow in an open source R package.\n\nContacthelena.herrmann@postgrad.manchester.ac.uk

microbiology↗

bioRxiv2017

Molecular Noise Accelerates Cell Division And Death Under Antibiotic Treatment

It is well known that microbial cell populations can exhibit sustained exponential growth. More surprising is the fact that at high antibiotic levels, cell populations exhibit sustained exponential decay over several orders of magnitude. The boundary between growth and decay occurs at the Minimal Inhibitory Concentration (MIC) of the antibiotic, where the density of living cells remains constant over time. These observations suggest that positive (growth) or negative (decay) exponents arise as a difference of cell division and death rates obeying first-order kinetics. Thus for antibiotic concentrations below MIC, division dominates; for concentrations above MIC, death dominates; while MIC itself is a dynamic steady state of balanced division and death, rather than cell stasis. To measure these rates we separately tracked living and dead cells in Escherichia coli populations treated with the ribosome-targeting antibiotic kanamycin. We found that cells divide rapidly even at MIC: inferred division and death rates at MIC are 0.6 times the antibiotic-free division rate. A stochastic model of cells as collections of self-replicating units we term \"widgets\" reproduces both steady-state and transient features of our experiments, and explains first-order exponential kinetics. In this model cell division and death rates at MIC can be tuned from low to high values by amplifying molecular noise in the synthesis, degradation and partitioning of the widgets. At extremely low noise, cells approach the classic bacteriostatic limit at MIC: neither dividing nor dying. Noise-induced division and death of cells following antibiotic treatment could increase the likelihood of sepsis and antibiotic resistance.

microbiology↗

bioRxiv2017

16S rRNA Gene Sequencing Reveals Site-Specific Signatures Of The Upper And Lower Airways Of Cystic Fibrosis Patients

RationaleChronic rhinosinusitis (CRS) is an inflammatory disorder of the sinonasal mucosa associated with microbial colonization. Metastasis of sinus microbiota into the lower airways is thought have significant implications in the development of chronic respiratory disease. However, this dynamic has not been thoroughly investigated in cystic fibrosis (CF) patients, where lower airway infections are the primary driver of patient mortality. Given the high prevalence of CRS in CF patients and the proposed infection dynamic between the upper and lower airways, a better understanding of sinus-lung continuum is warranted.\n\nObjectiveTo compare the microbiome of matched sinus mucus and lung sputum samples from CF subjects undergoing functional endoscopic sinus surgery (FESS) for treatment of CRS.\n\nMethodsMucus was isolated from the sinuses and lungs of twelve CF patients undergoing FESS. 16S ribosomal RNA gene sequencing was then performed to compare bacterial communities of the CF lung and sinus niches. Finally, functional profiling was performed to predict bacterial metagenomes from the 16S dataset, and was used to compare pathogenic bacterial phenotypes between the upper and lower airways.\n\nMeasurements and Main ResultsBacterial richness was comparable between airway sites, though sinus and lung environments differed in community evenness, with the sinuses harboring a higher prevalence of dominant microorganisms. Beta diversity metrics also revealed that samples clustered more consistently by airway niche rather than by individual. Finally, predicted metagenomes showed that anaerobic metabolism was enriched in the lung environment, while genes associated with both biofilm formation and Gram identity were not variable between sites.\n\nConclusionsSinus and lung microbiomes are distinct with respect to richness and evenness, while sinus communities have a higher incidence of a dominant taxon. Additionally, ordination analyses point to sinus and lung environments as being stronger determinants of microbial community structure than the individual patient. Finally, BugBase-predicted metagenomes revealed anaerobic phenotypes to be in higher abundance in the lung relative to the sinuses. Our findings indicate that while the paranasal sinuses and lungs may still comprise a unified airway in which lower airways are seeded by sinus microbiota, these discrete airway microenvironments harbor distinct bacterial communities.

microbiology↗

bioRxiv2017

Enterococcus faecalis Modulates Immune Activation And Slows Healing During Wound Infection

Enterococcus faecalis is one of most frequently isolated bacterial species in wounds yet little is known about its pathogenic mechanisms in this setting. Here, we used a mouse wound excisional model to characterize the infection dynamics of E. faecalis and show that infected wounds result in two different states depending on the initial inoculum. Low dose inocula were associated with short term, low titer colonization whereas high dose inocula were associated with acute bacterial replication and long term persistence. High dose infection and persistence were also associated with immune cell infiltration, despite suppression of some inflammatory cytokines and delayed wound healing. During high dose infection, the multiple peptide resistance factor (MprF) which is involved in resisting immune clearance, contributes to E. faecalis fitness. These results comprehensively describe a mouse model for investigating E. faecalis wound infection determinants, and suggest that both immune modulation and resistance contribute to persistent, non-healing wounds.

microbiology↗

bioRxiv2017

SMC Progressively Aligns Chromosomal Arms In Caulobacter crescentus But Is Antagonized By Convergent Transcription

The Structural Maintenance of Chromosomes (SMC) complex plays an important role in chromosome organization and segregation in most living organisms. In Caulobacter crescentus, SMC is required to align the left and the right arms of the chromosome that run in parallel down the long axis of the cell. However, the mechanism of SMC-mediated alignment of chromosomal arms remains elusive. Here, using a genome-wide chromosome conformation capture assay (Hi-C), chromatin immunoprecipitation with deep sequencing (ChIP-seq) and microscopy of single cells, we show that Caulobacter SMC is recruited to the centromeric parS site and that SMC-mediated arm alignment depends on the chromosome partitioning protein ParB. We provide evidence that SMC likely tethers the parS-proximal regions of the chromosomal arms together, promoting arm alignment. Strikingly, the co-orientation of DNA replication and the transcription of highly-expressed genes is crucial for chromosome-wide alignment. Highly-transcribed genes near parS that are oriented against DNA replication disrupt arm alignment suggesting that head-on transcription interferes with SMC translocation and arm alignment. Our results demonstrate a tight interdependence of bacterial chromosome organization and global patterns of transcription.

microbiology↗

bioRxiv2017

Microbial Community Assembly And Metabolite Profile Of The Gut Microbiome In Extremely Low Birthweight Infants

The assembly and development of the gut microbiome in infants has important consequences for immediate and long-term health. Preterm infants represent an abnormal case for bacterial colonization because of early exposure to bacteria and frequent use of antibiotics. To better understand the assembly of the gut microbiota in preterm infants, fecal samples were collected from 32 very low birthweight preterm infants over the first six weeks of life. Infant health outcomes included healthy, late-onset sepsis, and necrotizing enterocolitis (NEC). We characterized the bacterial composition by 16S rRNA gene sequencing and metabolome by untargeted gas chromatography mass spectrometry. Preterm infant fecal samples lacked beneficial Bifidobacterium and were dominated by Enterobacteriaceae, Enterococcus, and Staphylococcus due to the near uniform antibiotic administration. Most of the variance between the microbial community compositions could be attributed to which baby the sample came from (Permanova R2=0.48, p<0.001), while clinical status (healthy, NEC, or late-onset sepsis), and overlapping time in the NICU did not explain a significant amount of variation in bacterial composition. Fecal metabolomes were also found to be unique to the individual (Permanova R2=0.43, p<0.001) and weakly associated with bacterial composition (Mantel statistic r = 0.23 {+/-} 0.05 (p = 0.03 {+/-} 0.03). No measured metabolites were found to be associated with necrotizing enterocolitis, late-onset sepsis or a healthy outcome. Overall, preterm infants gut microbial communities were personalized and reflected antibiotic usage.\n\nImportancePreterm infants face health problems likely related to microbial exposures including sepsis and necrotizing enterocolitis. However, the role of the gut microbiome in preterm infant health is poorly understood. Microbial colonization differs from healthy term babies because it occurs in the NICU and is often perturbed by antibiotics. We measured bacterial compositions and metabolomic profiles of 77 fecal samples from thirty-two preterm infants to investigate the differences between microbiomes in health and disease. Rather than finding microbial signatures of disease, we found the preterm infant microbiome and metabolome were both personalized, and that the preterm infant gut microbiome is enriched in microbes that commonly dominate in the presence of antibiotics. These results contribute to the growing knowledge of the preterm infant microbiome and emphasize that a personalized view will be important to disentangling the health consequences of the preterm infant microbiome.

microbiology↗

bioRxiv2017

Sub-minute phosphoregulation of cell-cycle systems during Plasmodium gamete formation revealed by a high-resolution time course

Malaria parasites are protists of the genus Plasmodium, whose transmission to mosquitoes is initiated by the production of gametes. Male gametogenesis is an extremely rapid process that is tightly controlled to produce eight flagellated microgametes from a single haploid gametocyte within 10 minutes after ingestion by a mosquito. Regulation of the cell cycle is poorly understood in divergent eukaryotes like Plasmodium, where the highly synchronous response of gametocytes to defined chemical and physical stimuli from the mosquito has proved to be a powerful model to identify specific phosphorylation events critical for cell-cycle progression. To reveal the wider network of phosphorylation signalling in a systematic and unbiased manner, we have measured a high-resolution time course of the phosphoproteome of P. berghei gametocytes during the first minute of gametogenesis. The data show an extremely broad response in which distinct cell-cycle events such as initiation of DNA replication and mitosis are rapidly induced and simultaneously regulated. We identify several protein kinases and phosphatases that are likely central in the gametogenesis signalling pathway and validate our analysis by investigating the phosphoproteomes of mutants in two of them, CDPK4 and SRPK1. We show these protein kinases to have distinct influences over the phosphorylation of similar downstream targets that are consistent with their distinct cellular functions, which is revealed by a detailed phenotypic analysis of an SRPK1 mutant. Together, the results show that key cell-cycle systems in Plasmodium undergo simultaneous and rapid phosphoregulation. We demonstrate how a highly resolved time-course of dynamic phosphorylation events can generate deep insights into the unusual cell biology of a divergent eukaryote, which serves as a model for an important group of human pathogens.

microbiology↗

bioRxiv2017

Household triclosan and triclocarban exposure impacts the adult intestinal microbiome but not the infant intestinal microbiome

In 2016, the US Food and Drug Administration banned the use of specific microbicides in some household and personal wash products. This decision was due to concerns that these chemicals might induce antibiotic resistance or disrupt human microbial communities. Triclosan and triclocarban (referred to as TCs) are the most common antimicrobials in household and personal care products, but the extent to which TC exposure perturbs microbial communities in humans, particularly during infant development, was unknown. We conducted a randomized intervention of TC-containing household and personal care products during the first year following birth to characterize whether TC exposure from wash products perturbs microbial communities in mothers and their infants. Longitudinal survey of the intestinal microbiota using 16S ribosomal RNA amplicon sequencing showed that TC exposure from wash products did not induce global reconstruction of either infant or maternal intestinal microbiotas following 10 months of exposure after birth. However, broadly antibiotic-resistant species from the phylum Proteobacteria were enriched in stool samples from mothers in TC households only after the introduction of triclosan-containing toothpaste. Despite the minimal effects of TC exposure from wash products on the gut microbial community of infants and adults, these results suggest detected taxonomic differences are associated with potential harmful effects on host physiology, highlighting the need for consumer safety testing of self-care products not subject to the ban on the human microbiome and health outcomes.

microbiology↗

bioRxiv2017

Mupirocin-associated temporal changes in the nasal microbiota and host’s antimicrobial responses: A pilot study in healthy staphylococcal carriers

BackgroundHow mupirocin affects the human nasal microbiota over time remains uncharacterized.\n\nMethodsWe repeatedly sampled the anterior nares of four healthy staphylococcal carriers before and after mupirocin use. By sequencing bacterial 16S ribosomal cDNA, we characterized sequential changes in the carriage status, the nasal microbiota, and the hosts antimicrobial peptide expression up to 90 days after decolonization.\n\nResultsBefore mupirocin use, the nasal microbiota differed by the initial, culture-based staphylococcal carriage status, with Firmicutes (54.1%) being the most predominant in carriers and Proteobacteria (75.8%) in the only noncarrier. The nasal microbiota became less diverse (Shannon diversity: 1.33, 95% confidence interval [CI]: 1.06-1.54) immediately after decolonisation than that before decolonisation (1.78, 95%CI: 0.58-1.93). Based on results of differential abundance analysis, Firmicutes were significantly enriched (log2 fold changes [≥] 4, Benjamini-Hochberg adjusted P < .01) while Actinobacteria, particularly Corynbebacterium, were relatively depleted in samples from staphylococcal carriers. Results of nonmetric multidimensional scaling (NMDS) and constrained correspondence analysis (CCA) also suggested that the initial staphylococcal carriage status, human neutrophil peptide 1 levels, and sampling times were major contributors to the between-community dissimilarities (P for marginal permutation test: .014) though the significance attenuated when within-group correlation was considered (P for blocked permutation test: .047).\n\nConclusionThese findings suggest that large-scale investigations on antibiotic effects on the human nasal microbiota are warranted.

microbiology↗

bioRxiv2017

Genome Wide Identification Of Genes Required For Bacterial Plant Infection By Tn-Seq

Soft rot enterobacteria (Dickeya and Pectobacterium) are major pathogens that cause diseases on plants of agricultural importance such as potato and ornamentals. Long term studies to identify virulence factors of these bacteria focused mostly on plant cell wall degrading enzymes secreted by the type II secretion system and the regulation of their expression. To identify new virulence factors we performed a Tn-seq genome-wide screen of a transposon mutant library during chicory infection followed by high-throughput sequencing. This allowed the detection of mutants with reduced but also increased fitness in the plant. Virulence factors identified differed from those previously known since diffusible ones (secreted enzymes, siderophores or metabolites) were not detected by this screen. In addition to genes encoding proteins of unknown function that could be new virulence factors, others could be assigned to known biological functions. The central role of the FlhDC regulatory cascade in the control of virulence was highlighted with the identification of new members of this pathway. Scarcity of the plant in certain amino acids and nucleic acids required presence of the corresponding biosynthetic genes in the bacteria. Their products could be targets for the development of antibacterial compounds. Among the genes required for full development in chicory we also identified six genes involved in the glycosylation of the flagellin FliC, glycosylation, which in other plant pathogenic bacteria contributes to virulence.\n\nAuthor summaryIdentification of virulence factors of plant pathogenic bacteria has relied on the test of individual mutants on plants, a time-consuming method. New methods like transcriptomic or proteomic can now be used but they only allow the identification of genes induced during the infection process and non-induced genes may be missed. Tn-seq is a very powerful method to identify genes required for bacterial growth in their host. We used for the first time this method in a plant pathogenic bacteria to identify genes required for the multiplication of Dickeya dadantii in chicory. We identified about 100 genes with decreased or increased fitness in the plant. Most of them had no previously described role in bacterial virulence. We unveiled important metabolic genes and regulators of motility and virulence. We showed that D. dadantii flagellin is glycosylated and that this modification confers fitness to the bacteria during plant infection. Our work opens the way to the use of Tn-seq with bacterial phytopathogens. Assay by this method of large collections of environmental pathogenic strains now available will allow an easy and rapid identification of new virulence factors.

microbiology↗

bioRxiv2017

Individual Variation Of Natural D. melanogaster Associated Bacterial Communities

D. melanogaster has become an important model organism to study host-microbe interaction. However, we still know little about the natural microbial communities that are associated with D. melanogaster. Especially, information on inter-individual variation is still lacking because most studies so far have used pooled material from several flies. Here, we collected bacterial 16S rRNA gene community profiles from a set of 32 individuals from a single population and compare the variation to that of samples collected from different substrates and locations. While community differences were on average larger between samples collected from different substrates, there was still a surprising amount of variation of microbial communities between individual flies. The samples clustered into two groups suggesting that there are yet unknown factors that affect the composition of natural fly associated microbial communities and need research.\n\nImportanceD. melanogaster is an important model organism in evolutionary biology and also for the study of host-microbe interaction. In order to connect these to aspects of D. melanogaster biology, it is crucial to better understand the natural D. melanogaster microbiota because only the natural microbiota can affect the evolution of the host. We present, to our knowledge, the first data set that captures inter-individual variation of D. melanogaster associated bacterial communities. Clustering of communities into two larger groups suggests that there are important drivers of these communities that we do not understand yet suggesting in return that more research on the natural microbiota of D. melanogaster is needed.

microbiology↗

bioRxiv2017

Bacterial community composition and dynamics spanning five years in freshwater bog lakes

Bacteria play a key role in freshwater biogeochemical cycling, but long-term trends in freshwater bacterial community composition and dynamics are not yet well characterized. We used a multi-year time series of 16S rRNA gene amplicon sequencing data from eight bog lakes to census the freshwater bacterial community and observe annual and seasonal trends in abundance. Multiple sites and sampling events were necessary to begin to fully describe the bacterial communities. Each lake and layer contained a distinct bacterial community, with distinct levels of richness and indicator taxa that likely reflected the environmental conditions of each site. The community present in each year and site was also unique. Despite high interannual variability in community composition, we detected a core community of ubiquitous freshwater taxa. Although trends in abundance did not repeat annually, each freshwater lineage within the communities had a consistent lifestyle, defined by persistence, abundance, and variability. The results of our analysis emphasize the importance of long-term observations, as analyzing only a single year of data would not have allowed us to describe the dynamics and composition of these freshwater bacterial communities to the extent presented here.\n\nImportanceLakes are excellent systems for investigating bacterial community dynamics because they have clear boundaries and strong environmental gradients. The results of our research demonstrate that bacterial community dynamics operate on multi-year timescales, a finding which likely applies to other ecosystems, with implications for study design and interpretation. Understanding the drivers and controls of bacterial communities on long time scales would improve both our knowledge of fundamental properties of bacterial communities, and our ability to predict community states. In this specific ecosystem, bog lakes play a disproportionately large role in global carbon cycling, and the information presented here may ultimately help refine carbon budgets for these lakes. Finally, all data and code in this study are publicly available. We hope that this will serve as a resource to anyone seeking to answer their own microbial ecology questions using a multi-year time series.

microbiology↗

bioRxiv2017

Enhancing Multiplex Genome Editing by Natural Transformation (MuGENT) via inactivation of ssDNA exonucleases

Recently, we described a method for multiplex genome editing by natural transformation (MuGENT). Mutant constructs for MuGENT require large arms of homology (>2000 bp) surrounding each genome edit, which necessitates laborious in vitro DNA splicing. In Vibrio cholerae, we uncover that this requirement is due to cytoplasmic ssDNA exonucleases, which inhibit natural transformation. In ssDNA exonuclease mutants, one arm of homology can be reduced to as little as 40 bp while still promoting integration of genome edits at rates of ~50% without selection in cis. Consequently, editing constructs are generated in a single PCR reaction where one homology arm is oligonucleotide encoded. To further enhance editing efficiencies, we also developed a strain for transient inactivation of the mismatch repair system. As a proof-of-concept, we used these advances to rapidly mutate 10 high-affinity binding sites for the nucleoid occlusion protein SlmA and generated a duodecuple mutant of 12 diguanylate cyclases in V. cholerae. Whole genome sequencing revealed little to no off-target mutations in these strains. Finally, we show that ssDNA exonucleases inhibit natural transformation in Acinetobacter baylyi. Thus, rational removal of ssDNA exonucleases may be broadly applicable for enhancing the efficacy and ease of MuGENT in diverse naturally transformable species.

microbiology↗

bioRxiv2017

A Zebrafish Model For Mycobacterium leprae Granulomatous Infection

Understanding the pathogenesis of leprosy granulomas has been hindered by a paucity of tractable experimental animal models. Mycobacterium leprae, which causes leprosy, grows optimally at ~30{degrees}C, so we sought to model granulomatous disease in the ectothermic zebrafish. We find noncaseating granulomas develop rapidly, and eventually eradicate infection. rag1 mutant zebrafish, which lack lymphocytes, also form noncaseating granulomas with similar kinetics, but these control infection more slowly. Our findings establish the zebrafish as a facile, genetically tractable model for leprosy, and reveal the interplay between innate and adaptive immune determinants mediating leprosy granuloma formation and function.

microbiology↗

bioRxiv2017

Specific hypersensitive response-associated recognition of new apoplastic effectors from Cladosporium fulvum in wild tomato

Tomato leaf mould disease is caused by the biotrophic fungus Cladosporium fulvum. During infection, C. fulvum produces extracellular small secreted protein (SSP) effectors that function to promote colonization of the leaf apoplast. Resistance to the disease is governed by Cf immune receptor genes that encode receptor-like proteins (RLPs). These RLPs recognize specific SSP effectors to initiate a hypersensitive response (HR) that renders the pathogen avirulent. C. fulvum strains capable of overcoming one or more of all cloned Cf genes have now emerged. To combat these strains, new Cf genes are required. An effectoromics approach was employed to identify wild tomato accessions carrying new Cf genes. Proteomics and transcriptome sequencing were first used to identify 70 apoplastic in planta-induced C. fulvum SSPs. Based on sequence homology, 61 of these SSPs were novel or lacked known functional domains. Seven, however, had predicted structural homology to antimicrobial proteins, suggesting a possible role in mediating antagonistic microbe-microbe interactions in planta. Wild tomato accessions were then screened for HR-associated recognition of 41 SSPs using the Potato virus X-based transient expression system. Nine SSPs were recognized by one or more accessions, suggesting that these plants carry new Cf genes available for incorporation into cultivated tomato.

microbiology↗

bioRxiv2017

A Macrophage Response To Mycobacterium leprae Phenolic Glycolipid Initiates Nerve Damage In Leprosy

Mycobacterium leprae causes leprosy, and is unique among mycobacterial diseases in producing peripheral neuropathy. This debilitating morbidity is attributed to axon demyelination resulting from direct interactions of the M. leprae-specific phenolic glycolipid 1 (PGL-1) with myelinating glia, and their subsequent infection. Here, we use transparent zebrafish larvae to visualize the earliest events of M. leprae-induced nerve damage. We find that demyelination and axonal damage are not directly initiated by M. leprae but by infected macrophages that patrol axons; demyelination occurs in areas of intimate contact. PGL-1 confers this neurotoxic response on macrophages: macrophages infected with M. marinum expressing PGL-1 also damage axons. PGL-1 induces nitric oxide synthase in infected macrophages, and the resultant increase in reactive nitrogen species damages axons by injuring their mitochondria and inducing demyelination. Our findings implicate the response of innate macrophages to M. leprae PGL-1 in initiating nerve damage in leprosy.

microbiology↗

bioRxiv2017

Succession of embryonic and intestinal bacterial communities of Atlantic salmon

Host-associated microbiota undergoes continuous transition to achieve a stable community, and these modifications are immediately initiated from the birth of the host. In the present study, the succession of early life (eyed egg, embryo, and hatchling stages) and intestinal (the whole intestine at the early freshwater stages and the distal intestine at the late freshwater and seawater stages) bacterial communities of Atlantic salmon (Salmo salar; a prominent farmed fish) were studied using a 16S rRNA gene (V3 region) amplicon sequencing technique.\n\nStage-specific bacterial community compositions and the progressive transitions of the communities were evident in both the early life and the intestine. The embryonic communities were relatively less diverse, but after hatching the diversity increased significantly. A marked transition of the intestinal communities also occurred during the development. The most abundant functional pathways associated with the different stages were not affected by the transition of the community composition A perceptible transition in the community composition occurred during the development of Atlantic salmon. The transition generally did not alter the core functions of the community. Hatching and transfer to seawater are the key events that affect the bacterial diversity and community composition. The contribution of host-derived factors and environment in shaping the bacterial communities need to be confirmed through further studies.

microbiology↗

bioRxiv2017

Aging, Mortality And The Fast Growth Trade-Off Of Schizosaccharomyces pombe

Replicative aging has been demonstrated in asymmetrically dividing unicellular organisms, seemingly caused by unequal damage partitioning. Although asymmetric segregation and inheritance of potential aging factors also occurs in symmetrically dividing species, it nevertheless remains controversial whether this results in aging. Based on large-scale single-cell lineage data obtained by time-lapse microscopy with a microfluidic device, in this report, we demonstrate the absence of replicative aging in old-pole cell lineages of Schizosaccharomyces pombe cultured under constant favorable conditions. By monitoring more than 1,500 cell lineages in seven different culture conditions, we showed that both cell division and death rates are remarkably constant for at least 50-80 generations. Our measurements revealed that the death rate per cellular generation increases with division rate, pointing to a physiological trade-off with fast growth under balanced growth conditions. We also observed the formation and inheritance of Hsp104-associated protein aggregates, which are a potential aging factor in old-pole cell lineages, and found that these aggregates exhibited a tendency to preferentially remain at the old-poles for several generations. However, the aggregates were eventually segregated from old-pole cells upon cell division and probabilistically allocated to new-pole cells. The quantity and inheritance of protein aggregates increased neither cellular generation time nor cell death initiation rates. Furthermore, our results revealed that unusually large amounts of protein aggregates induced by oxidative stress exposure did not result in aging; old-pole cells resumed normal growth upon stress removal, despite the fact that most of them inherited significant quantities of aggregates. These results collectively indicate that protein aggregates are not a major determinant of cell fate in S. pombe, and thus cannot be an appropriate molecular marker or index for replicative aging under both favorable and stressful environmental conditions.

microbiology↗